library(terra)
library(tmap)
library(sf)
library(units)
#' Extract an RGB mask and optionally save outputs
#'
#' @param img_path path to RGB image (GeoTIFF, PNG, JPG)
#' @param thr list of R/G/B thresholds (each with min/max 0–255)
#' @param out_mask optional path to write binary raster (tif)
#' @param out_vect optional path to write polygons (gpkg/shp)
#'
#' @return a SpatRaster mask (1 = match, NA = no match)
#' @export
extract_rgb_mask <- function(img_path,
thr = list(
R = c(min = 0, max = 10),
G = c(min = 55, max = 70),
B = c(min = 70, max = 80)
),
out_mask = NULL,
out_vect = NULL) {
# --- load ---
x <- rast(img_path)
rgb <- x[[1:3]]
# scale to 0–255 if needed
rng <- global(rgb, range, na.rm = TRUE)
if (all(rng[, 2] <= 1.01, na.rm = TRUE)) {
rgb <- rgb * 255
}
names(rgb) <- c("R", "G", "B")
# build mask: 1 if within thresholds else NA
mask <- (rgb$R >= thr$R["min"] & rgb$R <= thr$R["max"]) &
(rgb$G >= thr$G["min"] & rgb$G <= thr$G["max"]) &
(rgb$B >= thr$B["min"] & rgb$B <= thr$B["max"])
mask <- classify(mask, cbind(0, NA)) # convert FALSE to NA, keep TRUE as 1
# write outputs if requested
if (!is.null(out_mask)) {
writeRaster(mask, out_mask, overwrite = TRUE)
}
if (!is.null(out_vect)) {
polys <- as.polygons(mask, dissolve = TRUE, values = TRUE, trunc = TRUE, na.rm = TRUE)
polys <- subset(polys, mask == 1, drop = TRUE)
writeVector(polys, out_vect, overwrite = TRUE)
}
mask
}
hook_tiff <- "/Users/rof011/Whitsundays/HookIsland_North2.tiff"
hayman_tiff <- "/Users/rof011/Whitsundays/HaymanIsland2.tiff"
hook_rgba <- rast(hook_tiff)
hayman_rgba <- rast(hayman_tiff)
hook_reef <- extract_rgb_mask(hook_tiff)
hayman_reef <- extract_rgb_mask(hayman_tiff)
hook_polys <- as.polygons(hook_reef, dissolve = TRUE, values = TRUE, trunc = TRUE, na.rm = TRUE) |> st_as_sf()
hayman_polys <- as.polygons(hayman_reef, dissolve = TRUE, values = TRUE, trunc = TRUE, na.rm = TRUE) |> st_as_sf()
whitsundays_reef <- rbind(hook_polys, hayman_polys) |> st_transform(4326)
